Comparison between SIR calibrated model outcomes and calibration targets

Code

library(here)
library(plotly)
source(here("02_scripts/01_fun_data.R"))
source(here("02_scripts/03a_fun_calib_td.R"))
source(here("03_outputs/03_map_calibmod_vs_targets_td.R"))

calib_samples <- readRDS(here("01_data/calib_samples_sir.RDS"))
uncalib_samples <- readRDS(here("01_data/uncalib_sample_sir.RDS"))

opt_params_sir_prev <- readRDS(here("01_data/prev_outcome_data_sir.RDS"))
opt_params_sir_deaths <- readRDS(here("01_data/death_outcome_data_sir.RDS"))
opt_params_sir_oddeaths <- readRDS(here("01_data/oddeath_outcome_data_sir.RDS"))
opt_params_sir_oat <- readRDS(here("01_data/oat_outcome_data_sir.RDS"))

params_sir_prev_uncalib <- readRDS(here("01_data/prev_outcome_data_sir_uncalib.RDS"))
params_sir_deaths_uncalib <- readRDS(here("01_data/death_outcome_data_sir_uncalib.RDS"))
params_sir_oddeaths_uncalib <- readRDS(here("01_data/oddeath_outcome_data_sir_uncalib.RDS"))
params_sir_oat_uncalib <- readRDS(here("01_data/oat_sir_uncalib.RDS"))

SIR calibration sample: first i sampled from prior 10000 sample sets, then i used them to calculated outcomes and likelihoods for each sample set, then i resampled from those 10000 with replacement with likelihood weights 10000 samples (unique sets = 6398), and ran the model on all of them and generated distributions for prevalence of rx opioid use, deaths, od deaths, total oat —- likelihood included deaths (gamma distribution), prevalence of rx opioid use (normal distribution instead of binomial), and total OAT

Uncalibrated sample: Here i resampled from the 10 000 sampled from the prior with replacement with equal weights 10000 sampled (unique sets = 6296), then ran the model on all of them and generated distributions for prevalence of rx opioid use, deaths, od deaths and total oat

1 Prevalence of Rx opioid use

Code

dt_prev <- as.data.frame(params_sir_prev_uncalib) %>% 
  pivot_longer(1:4, names_to = "prev_year", values_to = "value") %>% 
  mutate(group = "Uncalibrated Sample") %>% 
  bind_rows(., as.data.frame(opt_params_sir_prev) %>%
              pivot_longer(1:4, names_to = "prev_year", values_to = "value") %>% 
              mutate(group = "SIR Calibrated Sample"))

prev_year = c("yr15", "yr16", "yr17", "yr18")

wprop_opioids_rx_tbl <- prop_opioids_rx_target_tbl %>% 
  rename(value = target_val) %>% 
  mutate(grp = "Target",
         prev_year = ifelse(grepl("15", year_mon),2015,
                            ifelse(grepl("16", year_mon), 2016,
                                   ifelse(grepl("17", year_mon), 2017,
                                          ifelse(grepl("18", year_mon), 2018, year_mon)))),
         prev_year = factor(prev_year)) %>%
  select(-year_mon) %>% 
  bind_rows(., prop_opioids_rx_uncalib_tbl %>% 
               group_by(year) %>% 
               summarise(value = weighted.mean(target_val, tot_pop_val)) %>% 
               ungroup() %>% 
               mutate(prev_year = factor(year),
                      grp = "Uncalibrated Model - Point estimate")) %>% 
  bind_rows(., prop_opioids_rx_calib_tbl %>% 
               group_by(year) %>% 
               summarise(value = weighted.mean(target_val, tot_pop_val)) %>% 
               ungroup() %>% 
               mutate(prev_year = factor(year),
                      grp = "MAP Calibrated Model")) %>% 
  bind_rows(., dt_prev %>% 
              group_by(prev_year) %>% 
              summarize(value = mean(value)) %>% 
              mutate(grp = "SIR Calibrated Model - Mean",
                     prev_year = factor(prev_year))) %>% 
  bind_rows(., dt_prev %>% 
              group_by(prev_year) %>% 
              summarize(value = median(value)) %>% 
              mutate(grp = "SIR Calibrated Model - Median",
                     prev_year = factor(prev_year)))


ggplotly(ggplot(data = dt_prev,
       aes(y = value, x = prev_year)) +
  geom_violin(aes(fill = group), position = "dodge", alpha = 0.5) +
  geom_point(data = wprop_opioids_rx_tbl,
             aes(y = value, x = prev_year, color = grp))+
  xlab("Year") +
  scale_color_brewer(palette = "Set1", name = "") +
  scale_fill_brewer(palette = "Set1", name = "") +
  facet_wrap(~group))

Code

ggplotly(ggplot(data = dt_prev,
                        aes(x = value)) +
                   geom_histogram(aes(fill = group), color="#e9ecef",
                                  alpha=0.3, position = 'identity')  +
                   geom_vline(data = wprop_opioids_rx_tbl, aes(xintercept = value, color = grp))+
                   theme(axis.text.x = element_text(angle = 45)) +
                   xlab("Prevalence of rx opioids use") + ylab("") +
                   scale_color_brewer(palette = "Set1", name = "") +
                   scale_fill_brewer(palette = "Set1", name = "") +
                   facet_wrap(~prev_year, scales = "free"))

Code

p_prev_sir <- ggplot(data = dt_prev,
       aes(y = value, x = prev_year)) +
  geom_violin(aes(fill = group), position = "dodge", alpha = 0.5) +
  geom_point(data = wprop_opioids_rx_tbl,
             aes(y = value, x = prev_year, color = grp))+
  xlab("Year") +
  scale_color_brewer(palette = "Set1", name = "") +
  scale_fill_brewer(palette = "Set1", name = "") +
  facet_wrap(~group)
ggsave(here("04_report/p_prev_sir.png"))

2 Total Deaths

Code

dt_deaths <- as.data.frame(params_sir_deaths_uncalib) %>% 
  pivot_longer(1:5, names_to = "death_year", values_to = "value") %>% 
  mutate(group = "Uncalibrated Sample") %>% 
  bind_rows(., as.data.frame(opt_params_sir_deaths) %>% 
              pivot_longer(1:5, names_to = "death_year", values_to = "value") %>% 
              mutate(group = "SIR Calibrated Sample"))

ovrall_deaths_target_uncalib_tbl <- deaths_target_uncalib_tbl %>% 
  filter(target == "Total deaths") %>% 
  rename(value = target_val) %>% 
  mutate(grp = ifelse(group == "Calibrated Model", "MAP Calibrated Model",
                      ifelse(group == "Uncalibrated Model", "Uncalibrated Model - Point estimate",
                             ifelse(group == "Target", "Target", group))),
         death_year = factor(year)) %>% 
  select(-c(group, year)) %>% 
  bind_rows(., dt_deaths %>% 
              group_by(death_year) %>% 
              summarize(value = mean(value)) %>% 
              mutate(grp = "SIR Calibrated Model - Mean",
                     death_year = factor(death_year))) %>% 
  bind_rows(., dt_deaths %>% 
              group_by(death_year) %>% 
              summarize(value = median(value)) %>% 
              mutate(grp = "SIR Calibrated Model - Median",
                     death_year = factor(death_year)))


ggplotly(ggplot(data = dt_deaths, 
                aes(y = value, x = factor(death_year))) + 
           geom_violin(aes(fill = group), position = "dodge", alpha = 0.5) +
           geom_point(data = ovrall_deaths_target_uncalib_tbl,
                      aes(y = value, x = factor(death_year), color = grp))+
           xlab("Year") +
           scale_color_brewer(palette = "Set1", name = "") +
           scale_fill_brewer(palette = "Set1", name = "") +
           facet_wrap(~group))

Code

ggplotly(ggplot(data = dt_deaths,
                        aes(x = value/1000)) +
                   geom_histogram(aes(fill = group), color="#e9ecef",
                                  alpha=0.4, position = 'identity')  +
                   # scale_fill_manual(values=c("#69b3a2", "#404080")) +
                   geom_vline(data = ovrall_deaths_target_uncalib_tbl,
                              aes(xintercept = value/1000, color = grp))+
                   theme(axis.text.x = element_text(angle = 45)) +
                   xlab("Total deaths (in thousands)")+ ylab("") +
           scale_color_brewer(palette = "Set1", name = "") +
                   scale_fill_brewer(palette = "Set1", name = "") +
                   xlim(NA, 320)+
                   facet_wrap(~death_year, scales = "free"))

Code

p_deaths_sir <- ggplot(data = dt_deaths, 
                aes(y = value, x = factor(death_year))) + 
           geom_violin(aes(fill = group), position = "dodge", alpha = 0.5) +
           geom_point(data = ovrall_deaths_target_uncalib_tbl,
                      aes(y = value, x = factor(death_year), color = grp))+
           xlab("Year") +
           scale_color_brewer(palette = "Set1", name = "") +
           scale_fill_brewer(palette = "Set1", name = "") +
           facet_wrap(~group)
ggsave(here("04_report/p_deaths_sir.png"))

3 Opioid-related OD deaths

Code

dt_oddeaths <- as.data.frame(params_sir_oddeaths_uncalib) %>% 
  pivot_longer(1:6, names_to = "oddeath_year", values_to = "value") %>% 
  mutate(group = "Uncalibrated Sample") %>% 
  bind_rows(., as.data.frame(opt_params_sir_oddeaths) %>% 
              pivot_longer(1:6, names_to = "oddeath_year", values_to = "value") %>% 
              mutate(group = "SIR Calibrated Sample"))


od_deaths_target_uncalib_tbl <- deaths_target_uncalib_tbl %>% 
  filter(target == "Total OD-deaths") %>% 
  rename(value = target_val) %>% 
  mutate(grp = ifelse(group == "Calibrated Model", "MAP Calibrated Model",
                      ifelse(group == "Uncalibrated Model", "Uncalibrated Model - Point estimate",
                             ifelse(group == "Target", "Target", group))),
         oddeath_year = factor(year)) %>% 
  select(-c(group, year)) %>% 
  bind_rows(., dt_oddeaths %>% 
              group_by(oddeath_year) %>% 
              summarize(value = mean(value)) %>% 
              mutate(grp = "SIR Calibrated Model - Mean",
                     oddeath_year = factor(oddeath_year))) %>% 
  bind_rows(., dt_oddeaths %>% 
              group_by(oddeath_year) %>% 
              summarize(value = median(value)) %>% 
              mutate(grp = "SIR Calibrated Model - Median",
                     oddeath_year = factor(oddeath_year)))


ggplotly(ggplot(data = dt_oddeaths, 
                aes(y = value, x = factor(oddeath_year))) + 
           geom_violin(aes(fill = group), position = "dodge", alpha = 0.5) +
           geom_point(data = od_deaths_target_uncalib_tbl,
                      aes(y = value, x = factor(oddeath_year), color = grp))+
           xlab("Year") +
           scale_color_brewer(palette = "Set1", name = "") +
           scale_fill_brewer(palette = "Set1", name = "") +
           facet_wrap(~group))

Code

ggplotly(ggplot(data = dt_oddeaths,
                        aes(x = value)) +
                   geom_histogram(aes(fill = group), color="#e9ecef",
                                  alpha=0.4, position = 'identity')  +
                   geom_vline(data = od_deaths_target_uncalib_tbl,
                              aes(xintercept = value, color = grp))+
                   theme(axis.text.x = element_text(angle = 45)) +
                   xlab("Total opioid-related overdose deaths")+ ylab("") +
           scale_color_brewer(palette = "Set1", name = "") +
                   scale_fill_brewer(palette = "Set1", name = "") +
                   facet_wrap(~oddeath_year, scales = "free"))

Code

p_oddeath_sir <- ggplot(data = dt_oddeaths, 
                aes(y = value, x = factor(oddeath_year))) + 
           geom_violin(aes(fill = group), position = "dodge", alpha = 0.5) +
           geom_point(data = od_deaths_target_uncalib_tbl,
                      aes(y = value, x = factor(oddeath_year), color = grp))+
           xlab("Year") +
           scale_color_brewer(palette = "Set1", name = "") +
           scale_fill_brewer(palette = "Set1", name = "") +
           facet_wrap(~group)
ggsave(here("04_report/p_oddeath_sir.png"))

4 Total OAT counts

Code

dt_oat <- as.data.frame(params_sir_oat_uncalib) %>% 
  pivot_longer(1:length(2018:2021), names_to = "oat_year", values_to = "value") %>% 
  mutate(group = "Uncalibrated Sample") %>% 
  bind_rows(., as.data.frame(opt_params_sir_oat) %>% 
              pivot_longer(1:length(2018:2021), names_to = "oat_year", values_to = "value") %>% 
              mutate(group = "SIR Calibrated Sample"))

oat_target_uncalib_tbl <- oat_target_uncalib_tbl %>% 
  rename(value = target_val) %>% 
  mutate(grp = ifelse(group == "Calibrated Model", "MAP Calibrated Model",
                      ifelse(group == "Uncalibrated Model", "Uncalibrated Model - Point estimate",
                             ifelse(group == "Target", "Target", group))),
         oat_year = factor(year)) %>% 
  select(-c(group, year)) %>% 
  bind_rows(., dt_oat %>% 
              group_by(oat_year) %>% 
              summarize(value = mean(value)) %>% 
              mutate(grp = "SIR Calibrated Model - Mean",
                     oat_year = factor(oat_year))) %>% 
  bind_rows(., dt_oat %>% 
              group_by(oat_year) %>% 
              summarize(value = median(value)) %>% 
              mutate(grp = "SIR Calibrated Model - Median",
                     oat_year = factor(oat_year)))



ggplotly(ggplot(data = dt_oat, 
                aes(y = value, x = factor(oat_year))) + 
           geom_violin(aes(fill = group), position = "dodge", alpha = 0.5) +
           geom_point(data = oat_target_uncalib_tbl,
                      aes(y = value, x = factor(oat_year), color = grp))+
           xlab("Year") +
           scale_color_brewer(palette = "Set1", name = "") +
           scale_fill_brewer(palette = "Set1", name = "") +
           facet_wrap(~group))

Code

ggplotly(ggplot(data = dt_oat,
                        aes(x = value)) +
                   geom_histogram(aes(fill = group), color="#e9ecef",
                                  alpha=0.4, position = 'identity')  +
                   geom_vline(data = oat_target_uncalib_tbl,
                              aes(xintercept = value, color = grp))+
                   theme(axis.text.x = element_text(angle = 45)) +
                   xlab("Total OAT")+ ylab("") +
           scale_color_brewer(palette = "Set1", name = "") +
                   scale_fill_brewer(palette = "Set1", name = "") +
                   facet_wrap(~oat_year, scales = "free"))

Code

p_oat_sir <- ggplot(data = dt_oat, 
                aes(y = value, x = factor(oat_year))) + 
           geom_violin(aes(fill = group), position = "dodge", alpha = 0.5) +
           geom_point(data = oat_target_uncalib_tbl,
                      aes(y = value, x = factor(oat_year), color = grp))+
           xlab("Year") +
           scale_color_brewer(palette = "Set1", name = "") +
           scale_fill_brewer(palette = "Set1", name = "") +
           facet_wrap(~group)

ggsave(here("04_report/p_oat_sir.png"))